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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   STRUCTURAL ANALYSIS OF THE VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA SUBUNIT FUNCTIONAL CORE IN COMPLEX WITH ALPHA1 INTERACTION DOMAIN

Authors :   Y. Opatowsky, C. -C. Chen, K. P. Campbell, J. A. Hirsch

Date :   27 Apr 04 (Deposition) - 25 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein-Peptide Complex, Sh3 Domain, Guanylate Kinase Domain, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Opatowsky, C. -C. Chen, K. P. Campbell, J. A. Hirsch
Structural Analysis Of Voltage-Dependent Calcium Channel Beta Subunit Functional Core And Its Complex With The Alpha1 Interaction Domain
Neuron V. 42 387 2004
PubMed-ID: 15134636 | Reference-DOI: 10.1016/S0896-6273(04)00250-8
(for further references see the PDB file header)

Molecule 1 - DIHYDROPYRIDINE-SENSITIVE L-TYPE, CALCIUM CHANNEL BETA-2 SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	FUNCTIONAL CORE (RESIDUES 25-422)
	Gene	:	CACNB2, CACNLB2
	Mutation	:	YES
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	VOLTAGE-DEPENDENT CALCIUM CHANNEL BETA-2 SUBUNIT, CAB2

Molecule 2 - VOLTAGE-DEPENDENT L-TYPE CALCIUM CHANNEL ALPHA- 1S SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Fragment	:	AID
	Other Details	:	THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS FROM ORYCTOLAGUS CUNICULUS (RABBIT) GENE CACNA1S.
	Synonym	:	CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE, ISOFORM 3, SKELETAL MUSCLE
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1T3L)

(no "Site" information available for 1T3L)

(no "SS Bond" information available for 1T3L)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:234	-	Pro A:235

(no "SAP(SNP)/Variant" information available for 1T3L)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SH3	PS50002	Src homology 3 (SH3) domain profile.	CACB2_RABIT	86-147	1	A:60-121

(no "Exon" information available for 1T3L)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:306
 aligned with CACB2_RABIT | P54288 from UniProtKB/Swiss-Prot  Length:632

    Alignment length:382
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439  
          CACB2_RABIT    60 LEEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVSYSAAHEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSPVKLENMRLQHEQRAKQGKFYSSKSGGNSSSSLGDIVPSSRKSTPPSSAIDIDATGLDAEENDIPANHRSPKPSANSVTSPHSKEKRMPFFKKTEHTPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIVVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPELFDVILDENQLEDACEHLADYLEAYWKATHPPSS 441
               SCOP domains -d1t3la1 A:35-141 SH3-like domain of the L-type calcium channel                                             ----------------------------------------------------------------------------d1t3la2 A:218-415 Guanylate kinase-like domain of the L-type calcium channel                                                                                                                           SCOP domains
               CATH domains 1t3lA01 A:34-140,A:218-225 SH3 Domains                                                                     -----------------------------------------------------------------------------1t3lA01 1t3lA02 A:226-415 P-loop containing nucleotide triphosphate hydrolases                                                                                                                         CATH domains
               Pfam domains VGCC_beta4Aa_N-1t3lA02    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------Guanylate_kin-1t3lA01 A:226-406                                                                                                                                                      --------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.........................eeeeeee....eeeeee.......eeeehhhhhhhhhhhhhhhhhhh..----------------------------------------------------------------------------...eeee.....eeee......hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhhhhh....eeeeee....hhhhh.......eeeee...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.eee...hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------SH3  PDB: A:60-121 UniProt: 86-147                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t3l A  34 LEEDREAVRREAERQAQAQLEKAKTKPVAFAVRTNVSYSAAHEDDVPVPGMAISFEAKDFLHVKEKFNNDWWIGRLVKEGCEIGFIPSRVKLENMRLQHEQRAKEFKL----------------------------------------------------------------------------TPPYDVVPSMRPVVLVGPSLKGYEVTDMMQKALFDFLKHRFEGRISITRVTADISLAKRSVLNNPSKHAIIERSNTRSSLAEVQSEIERIFELARTLQLVVLDADTINHPAQLSKTSLAPIVVYVKISSPKVLQRLIKSRGKSQAKHLNVQMVAADKLAQCPPELFDVILDENQLEDACEHLADYLEAYWKATHPPSS 415
                                    43        53        63        73        83        93       103       113       123       133       | -         -         -         -         -         -         -         -    |  223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413  
                                                                                                                                     141                                                                          218

Chain B from PDB  Type:PROTEIN  Length:17
 aligned with CAC1S_RABIT | P07293 from UniProtKB/Swiss-Prot  Length:1873

    Alignment length:17
                                   367       
          CAC1S_RABIT   358 QLEEDLRGYMSWITQGE 374
               SCOP domains d1t3lb_ B:        SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 1t3l B 358 QLEEDLRGYMSWITQGE 374
                                   367

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Rabbit (Oryctolagus cuniculus) (2)

1t3lA02

A:226-415

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Rabbit (Oryctolagus cuniculus) (2)

1t3lA01

A:34-140,A:218-225

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Guanylate_kin (23)

Oryctolagus cuniculus (Rabbit) (2)

Guanylate_kin-1t3lA01

A:226-406

Clan: no clan defined [family: VGCC_beta4Aa_N] (6)

Family: VGCC_beta4Aa_N (6)

Oryctolagus cuniculus (Rabbit) (2)

VGCC_beta4Aa_N-1t3lA02

A:34-59

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CACB2_RABIT | P54288)

molecular function
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
	GO:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0042383	sarcolemma	The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
	GO:0005891	voltage-gated calcium channel complex	A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

Chain B (CAC1S_RABIT | P07293)

molecular function
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
	GO:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005891	voltage-gated calcium channel complex	A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Sites
(no "Sites" information available for 1t3l)

	Cis Peptide Bonds
		Gly A:234 - Pro A:235	[ RasMol ]

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	1t3l
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	CACB2_RABIT \| P54288
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UniProtKB/Swiss-Prot
	CAC1S_RABIT \| P07293	:	1du1 1jzp 3jbr 5gjv 5gjw
	CACB2_RABIT \| P54288	:	1t3s 4dex 4dey

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 3)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (17, 28)

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